@sjcrh/proteinpaint-server 2.95.0 → 2.96.1

package/dataset/termdb.test.js

@@ -6,8 +6,6 @@ var termdb_test_default = {
   isMds3: true,
   cohort: {
     massNav: {
-      title: { text: "" },
-      //it will show cohorts instead
       tabs: {
         // about: {
         // 	hide: true,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-server",
-  "version": "2.95.0",
+  "version": "2.96.1",
   "type": "module",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "main": "src/app.js",
@@ -60,8 +60,8 @@
   "dependencies": {
     "@sjcrh/augen": "2.87.0",
     "@sjcrh/proteinpaint-rust": "2.84.0",
-    "@sjcrh/proteinpaint-shared": "2.95.0",
-    "@sjcrh/proteinpaint-types": "2.95.0",
+    "@sjcrh/proteinpaint-shared": "2.96.0",
+    "@sjcrh/proteinpaint-types": "2.96.1",
     "better-sqlite3": "^9.4.1",
     "body-parser": "^1.15.2",
     "canvas": "~2.11.2",

package/routes/termdb.boxplot.js

@@ -117,6 +117,9 @@ function init({ genomes }) {
         setHiddenPlots(q.tw, plots);
       if (overlayTerm && overlayTerm.term?.values)
         setHiddenPlots(overlayTerm, plots);
+      if (q.orderByMedian == true) {
+        plots.sort((a, b) => a.boxplot.p50 - b.boxplot.p50);
+      }
       const returnData = {
         absMin,
         absMax,
@@ -177,7 +180,7 @@ function setUncomputableValues(values) {
     return null;
 }
 function numericBins(overlayTerm, data) {
-  const overlayBins = data.refs.byTermId[overlayTerm?.term?.id]?.bins ?? [];
+  const overlayBins = data.refs.byTermId[overlayTerm?.$id]?.bins ?? [];
   return new Map(overlayBins.map((bin) => [bin.label, bin]));
 }
 export {

package/routes/termdb.singlecellSamples.js

@@ -54,7 +54,7 @@ async function validate_query_singleCell(ds, genome) {
   if (q.samples.src == "gdcapi") {
     gdc_validate_query_singleCell_samples(ds, genome);
   } else if (q.samples.src == "native") {
-    validateSamplesNative(q.samples, ds);
+    validateSamplesNative(q.samples, q.data, ds);
   } else {
     throw "unknown singleCell.samples.src";
   }
@@ -78,20 +78,40 @@ async function validate_query_singleCell(ds, genome) {
     validate_query_singleCell_DEgenes(ds);
   }
 }
-async function validateSamplesNative(S, ds) {
-  const samples = {};
+async function validateSamplesNative(S, D, ds) {
+  const samples = /* @__PURE__ */ new Map();
+  for (const plot of D.plots) {
+    try {
+      for (const fn of await fs.promises.readdir(path.join(serverconfig.tpmasterdir, plot.folder))) {
+        let sampleName = fn;
+        if (plot.fileSuffix) {
+          if (!fn.endsWith(plot.fileSuffix))
+            continue;
+          sampleName = fn.split(plot.fileSuffix)[0];
+        }
+        if (!sampleName)
+          continue;
+        const sid = ds.cohort.termdb.q.sampleName2id(sampleName);
+        if (sid == void 0)
+          continue;
+        samples.set(sid, { sample: sampleName });
+      }
+    } catch (e) {
+      console.log("cannot readdir on singleCell.data.plot[].folder", e);
+    }
+  }
   if (S.sampleColumns) {
     for (const term of S.sampleColumns) {
       const s2v = ds.cohort.termdb.q.getAllValues4term(term.termid);
-      for (const [s, v] of s2v.entries()) {
-        if (!samples[s])
-          samples[s] = { sample: ds.cohort.termdb.q.id2sampleName(s) };
-        samples[s][term.termid] = v;
+      for (const [sid, v] of s2v.entries()) {
+        if (!samples.has(sid))
+          continue;
+        samples.get(sid)[term.termid] = v;
       }
     }
   }
   S.get = () => {
-    return { samples: Object.values(samples) };
+    return { samples: [...samples.values()] };
   };
 }
 function validateDataNative(D, ds) {
@@ -227,6 +247,9 @@ function gdc_validateGeneExpression(G, ds, genome) {
   G.get = async (q) => {
     try {
       const fileid = q.sample.eID;
+      if (ds.__gdc.scrnaAnalysis2hdf5.size == 0) {
+        throw "GDC scRNA file mapping is not cached";
+      }
       const hdf5id = ds.__gdc.scrnaAnalysis2hdf5.get(fileid);
       if (!hdf5id)
         throw "cannot map eID to hdf5 id";

package/routes/termdb.topVariablyExpressedGenes.js

@@ -184,7 +184,7 @@ function gdcValidateQuery(ds, genome) {
     const { host, headers } = ds.getHostHeaders(q);
     try {
       const response = await cachedFetch(
-        joinUrl(host.geneExp, "/gene_expression/gene_selection"),
+        joinUrl(host.rest, "/gene_expression/gene_selection"),
         {
           method: "POST",
           headers,